Transcriptomics

Training material for all kinds of transcriptomics analysis.

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.

Requirements

Before diving into this topic, we recommend you to have a look at:

Material

Introduction

Start here if you are new to RNA-Seq analysis in Galaxy

Lesson Slides Hands-on Recordings Input dataset Workflows
Introduction to Transcriptomics
Reference-based RNA-Seq data analysis
De novo transcriptome reconstruction with RNA-Seq

End-to-End Analysis

These tutorials take you from raw sequencing reads to pathway analysis

Lesson Slides Hands-on Recordings Input dataset Workflows
1: RNA-Seq reads to counts
2: RNA-seq counts to genes
3: RNA-seq genes to pathways

Visualisation

Tutorials covering data visualisation

Lesson Slides Hands-on Recordings Input dataset Workflows
RNA Seq Counts to Viz in R
Visualization of RNA-Seq results with CummeRbund
Visualization of RNA-Seq results with Volcano Plot
Visualization of RNA-Seq results with Volcano Plot in R
Visualization of RNA-Seq results with heatmap2

Other

Assorted Tutorials

Lesson Slides Hands-on Recordings Input dataset Workflows
CLIP-Seq data analysis from pre-processing to motif detection
Differential abundance testing of small RNAs
GO Enrichment Analysis
Genome-wide alternative splicing analysis
Network analysis with Heinz
RNA-RNA interactome data analysis
RNA-Seq analysis with AskOmics Interactive Tool
RNA-seq Alignment with STAR
Small Non-coding RNA Clustering using BlockClust
Whole transcriptome analysis of Arabidopsis thaliana

Galaxy instances

You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.

You can also use the following Docker image for these tutorials:

docker run -p 8080:80 quay.io/galaxy/transcriptomics-training

NOTE: Use the -d flag at the end of the command if you want to automatically download all the data-libraries into the container.

It will launch a flavored Galaxy instance available on http://localhost:8080. This instance will contain all the tools and workflows to follow the tutorials in this topic. Login as admin with password password to access everything.

Frequently Asked Questions

Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.

Editorial Board

This material is reviewed by our Editorial Board:

orcid logoBérénice Batut avatar Bérénice Batutorcid logoMaria Doyle avatar Maria Doyleorcid logoFlorian Heyl avatar Florian Heyl

For any question related to this topic and the content, you can contact them or visit our Gitter channel.

Contributors

This material was contributed to by:

Daniel Maticzka avatar Daniel Maticzkaorcid logoCristóbal Gallardo avatar Cristóbal GallardoBelinda Phipson avatar Belinda PhipsonHarriet Dashnow avatar Harriet DashnowAnton Nekrutenko avatar Anton Nekrutenkoorcid logoClemens Blank avatar Clemens BlankXi Liu avatar Xi Liuorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoMo Heydarian avatar Mo HeydarianOlivier Dameron avatar Olivier Dameronorcid logoNicola Soranzo avatar Nicola SoranzoThe Carpentries avatar The Carpentriesorcid logoToby Hodges avatar Toby HodgesShian Su avatar Shian SuAndrea Bagnacani avatar Andrea Bagnacaniorcid logoErwan Corre avatar Erwan Correorcid logoMaria Doyle avatar Maria Doyleorcid logoMateo Boudet avatar Mateo Boudetorcid logoLucille Delisle avatar Lucille Delisleorcid logoMallory Freeberg avatar Mallory FreebergXavier Garnier avatar Xavier Garnierorcid logoHelena Rasche avatar Helena RascheJovana Maksimovic avatar Jovana MaksimovicCharity Law avatar Charity Laworcid logoAnika Erxleben avatar Anika Erxlebenorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosMarkus Wolfien avatar Markus WolfienAnna Trigos avatar Anna TrigosGildas Le Corguillé avatar Gildas Le Corguilléorcid logoSaskia Hiltemann avatar Saskia HiltemannChao Zhang avatar Chao ZhangAnne Siegel avatar Anne SiegelIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoPeter van Heusden avatar Peter van HeusdenMatt Ritchie avatar Matt Ritchieorcid logoBérénice Batut avatar Bérénice Batutorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoFlorian Heyl avatar Florian HeylJames Taylor avatar James Taylor

Funders

This material was funded by:

Gallantries: Bridging Training Communities in Life Science, Environment and Health avatar Gallantries

References